From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Aug 21 2014 - 03:04:01 CDT
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Maxime Boissonneault
> Gesendet: Mittwoch, 20. August 2014 16:20
> An: Norman Geist; 'Phil Greer'
> Cc: Namd Mailing List
> Betreff: Re: AW: namd-l: "Beefier" benchmark
>
> Le 2014-08-20 02:38, Norman Geist a écrit :
> > Hi,
> >
> > the timings you get with 0.01 s/step doesn't seem to be very good.
> Before
> > you move to a higher benchmark pls try in namd script:
> >
> > twoawayx yes
> >
> > if the above helps also try in addition:
> >
> > twoawayy yes
> >
> > if that helps try in addition:
> >
> > twoawayz yes
> >
> > This options artificially increase the number of patches (box slices)
> so
> > that the large amount of cores a GPU has can be better utilized.
> Any one of those reduces the time to 0.0074s/step.
> Any two of those makes the time ~0.0087s/step
> If I put all 3, the time goes up to 0.013s/step
Which combination brings improvement depends on system size. The smaller the
system, the better the benefit.
Keep the order x y z until benefit is gone. This needs to be tested for
different system sizes.
Also check if you still get speedup while increasing the number of GPUs. You
might already scale out much earlier, as this timing still doesn't represent
10 GPUs IMHO, guess 2 would do the same.
What value do you use for fullelectfrequency ?
>
> So, those parameters do not change the results ?
No, not more than the parallel execution anyway.
> > Also to the namd2 command try:
> >
> > +ignoresharing
> This either does not make a difference or slightly increase the times.
>
>
> Thanks,
>
> Maxime
>
> >
> > To come back to your original question, the stmv benchmark is quite
> large.
> >
> > Mit freundlichen Grüßen
> >
> > Norman Geist.
> >
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> >> Auftrag von Phil Greer
> >> Gesendet: Dienstag, 19. August 2014 18:31
> >> An: Maxime Boissonneault
> >> Cc: Namd Mailing List
> >> Betreff: Re: namd-l: "Beefier" benchmark
> >>
> >> Sometimes, the number of seconds/step is off if the run completes
> too
> >> quickly. This happened on a GPU system we were building in my
> >> department. Increasing the number of steps gives a bigger sample for
> >> computing seconds per step. In reality, that is just a fist pass
> test
> >> without finding a bigger system. If it is still claiming ~0.01s/step
> >> then a bigger system is needed.
> >>
> >> -Phil Greer
> >>
> >> On Aug 19, 2014, at 12:14 PM, Maxime Boissonneault
> >> <maxime.boissonneault_at_calculquebec.ca> wrote:
> >>
> >>> That will increase the total run time, but why would it change the
> >> number of seconds per step ?
> >>> Maxime Boissonneault
> >>>
> >>> Le 2014-08-19 12:10, Phil Greer a écrit :
> >>>> In the apoa1.namd file edit the numsteps parameter to 10000 or
> >> higher.
> >>>> -Phil Greer
> >>>>
> >>>> On Aug 19, 2014, at 11:48 AM, Maxime Boissonneault
> >> <maxime.boissonneault_at_calculquebec.ca> wrote:
> >>>>> Hi,
> >>>>> I am running the apoa1 benchmark on our GPU cluster. Each node
> has
> >> 8 GPUs and 20 cores. I am compiling Namd with MPI and SMP support.
> It
> >> seems I reach a limit of about ~0.01s/step with one node, and cannot
> go
> >> quicker with more than one node.
> >>>>> Is there a larger benchmark out there that would scale better on
> >> this type of system ?
> >>>>> Thanks,
> >>>>>
> >>>>> --
> >>>>> ---------------------------------
> >>>>> Maxime Boissonneault
> >>>>> Analyste de calcul - Calcul Québec, Université Laval
> >>>>> Ph. D. en physique
> >>>>>
> >>>
> >
> >
> > ---
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>
>
> --
> ---------------------------------
> Maxime Boissonneault
> Analyste de calcul - Calcul Québec, Université Laval
> Ph. D. en physique
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